Before PDE – Exporting copy the Plug-In Project into a temporary second Plug-In and merge all src – folders into the one and only /src root folder. (Now the workflow while developing and testing isn’t as easy as before)

Instead of PDE Export you can use a normal Java – Export as JAR (Loosing the comfort from PDE to auto-detect the Manifest file, versioning ….)

Create some ANT Tasks…

But I’m still looking for the pure PDE solution. Perhaps anyone has an idea how to make PDE happy with nested src folders ?